Modeling Intracellular Transport during Messenger RNA Localization in Xenopus Oocytes
Ciocanel, Maria-Veronica (creator)
Sandstede, Bjorn (Advisor)
Maxey, Martin (Reader)
McKinley, Scott (Reader)
Brown University. Department of Applied Mathematics (sponsor)
Many organisms need to establish spatial orientation during early development. In egg cells (oocytes) of the frog Xenopus laevis, spatial differentiation is achieved by localization of messenger RNA (mRNA), as these molecules move from the nucleus to the periphery of the egg cell during egg formation. Our goal is to understand how the long-term dynamics of mRNA molecules varies across the oocyte and how localization is regulated in space and time given parameters estimated using fluorescence recovery after photobleaching (FRAP) data. Although a large number of analytical and numerical models have been developed to extract binding and diffusion rates from FRAP recovery curves, active transport of molecules is typically not included in the existing models. We introduced a validated numerical method for estimating diffusion, binding/unbinding rates, and active transport velocities using FRAP data that captures intracellular dynamics through partial differential equation models. Given knowledge of these parameters, the effective velocity and diffusion of particles at large times are derived for linear and nonlinear PDE models of active transport using dynamical systems and stochastic methods. In combination with FRAP parameter estimates and predicted run times and lengths of particles, these asymptotic quantities quantify dynamical properties of localizing and non-localizing mRNA. Our results confirm the hypothesis of distinct transport dynamics in different regions of the egg cell and suggest that bidirectional transport of mRNA may influence the timescale of RNA localization in Xenopus oocytes. In addition, the parameter estimates inform numerical simulations of mRNA localization on model microtubule structures, which suggest that an anchoring mechanism at the cell periphery may be essential in reproducing localization patterns.